{
  "abstract": "The primary aim of this study was to determine whether metagenomic next-generation sequencing (mNGS) can identify potential microbial agents responsible for encephalitis of unknown origin in immunocompetent patients, thereby enhancing clinical diagnostics. Cerebrospinal fluid samples from well-characterized patients (n = 17) diagnosed with encephalitis of unknown origin, according to Swedish national guidelines, were sequenced using mNGS using the Ion Torrent platform and analyzed using bioinformatic platforms. Samples from patients with known viral CNS infections i.e. HSV-2 meningitis (n = 4), VZV CNS infections (n = 3), enterovirus meningitis (n = 2), JCV CNS infection (n = 2) were used as controls for the methodology (n = 11). No viral agents were detected in 16/17 CSF samples from patients with encephalitis of unknown etiology. 13/17 CSF samples were analysed for the most common autoimmune antibodies and were negative. In one CSF sample from patients with encephalitis of unknown origin a Human pegivirus (HPgV) was detected. In 9/11 control CSF samples from patients with CNS infections, RNA or DNA of the known virus were detected. The main conclusion in this study was that the negative results were related to that the majority of included patients were immunocompetent. The finding of HPgV in a patient with unknown encephalitis was judged as a bystander. However, mNGS might detect more pathogens in other patient cohorts and this study implicates that a close collaboration between the clinical laboratory and the clinicians enables a safe implementation of metagenomics.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden",
    "Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden",
    "Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden",
    "Bioinformatics and Data Centre, University of Gothenburg, Gothenburg, Sweden"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Erika Stentoft"
    },
    {
      "affs": [
        1
      ],
      "name": "Josefin Olausson"
    },
    {
      "affs": [
        2
      ],
      "name": "Emilio Rudbeck"
    },
    {
      "affs": [
        3
      ],
      "name": "Marie Studahl"
    },
    {
      "name": "Hedvig E. Jakobsson"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7dzrzr3c92hnr.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0358189",
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  "id": "7dzrzr3c92hnr",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0358189",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2725|Infectious Encephalopathies and Encephalitis"
    ],
    [
      "plos",
      "/Biology and life sciences/Anatomy/Body fluids/Cerebrospinal fluid"
    ],
    [
      "plos",
      "/Biology and life sciences/Anatomy/Nervous system/Central nervous system"
    ],
    [
      "plos",
      "/Biology and life sciences/Anatomy/Nervous system/Cerebrospinal fluid"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens/Herpesviruses/Epstein-Barr virus"
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      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
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    [
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      "/Biology and life sciences/Organisms/Viruses/Viral pathogens/Herpesviruses/Epstein-Barr virus"
    ],
    [
      "plos",
      "/Biology and life sciences/Physiology/Body fluids/Cerebrospinal fluid"
    ],
    [
      "plos",
      "/Medicine and health sciences/Anatomy/Body fluids/Cerebrospinal fluid"
    ],
    [
      "plos",
      "/Medicine and health sciences/Anatomy/Nervous system/Central nervous system"
    ],
    [
      "plos",
      "/Medicine and health sciences/Anatomy/Nervous system/Cerebrospinal fluid"
    ],
    [
      "plos",
      "/Medicine and health sciences/Diagnostic medicine"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Infectious diseases of the nervous system/Encephalitis"
    ],
    [
      "plos",
      "/Medicine and health sciences/Neurology/Infectious diseases of the nervous system/Encephalitis"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens/Herpesviruses/Epstein-Barr virus"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Bioinformatics"
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    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
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      "plos",
      "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/RNA sequencing"
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  "openalex": "W7213304685",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-15",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/7dzrzr3c92hnr.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:49Z",
      "native_id": "10.1371/journal.pone.0358189",
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      "url": "https://doi.org/10.1371/journal.pone.0358189"
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  "subjects": [
    {
      "field": "medicine",
      "origin": "plos:anatomy",
      "subfield": "physiology"
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  "title": "Metagenomic sequencing in encephalitis diagnostics: Challenges and opportunities in clinical settings",
  "title_text": "Metagenomic sequencing in encephalitis diagnostics: Challenges and opportunities in clinical settings",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:49Z",
  "url": "https://research.draconitic.com/paper/7dzrzr3c92hnr",
  "venue": "PLOS One",
  "versions": []
}